The replacement of the furanose moiety of DNA by a cyclohexene ring gives a new nucleic acid structure: cyclohexene nucleic acids or CeNA. CeNAs can be obtained by the classical phosphoramidite chemisty starting from protected cyclohexenyl nucleoside building blocks. Incorporation of cylcohexenyl nucleosides in a DNA chain increases the stability of a DNA/RNA hybrid. The complex formed between cyclohexenyl oligoadenylate and its DNA or RNA complement is of similar stability. Circular dichroism (CD) and NMR studies indicate easy conformational adaptation of a cyclohexenyl nucleoside when incorporated in a natural nucleic acid structure. CeNA is stable against degradation in serum and a CeNA/RNA hybrid is able to activate E. Coli RNase H, resulting in cleavage of the RNA strand.

Molecular dynamics (MD) simulations have become increasingly useful in the modern drug development process. In this review, we give a broad overview of the current application possibilities of MD in drug discovery and pharmaceutical development. Starting from the target validation step of the drug development process, we give several examples of how MD studies can give important insights into the dynamics and function of identified drug targets such as sirtuins, RAS proteins, or intrinsically disordered proteins. The role of MD in antibody design is also reviewed. In the lead discovery and lead optimization phases, MD facilitates the evaluation of the binding energetics and kinetics of the ligand-receptor interactions, therefore guiding the choice of the best candidate molecules for further development. The importance of considering the biological lipid bilayer environment in the MD simulations of membrane proteins is also discussed, using G-protein coupled receptors and ion channels as well as the drug-metabolizing cytochrome P450 enzymes as relevant examples. Lastly, we discuss the emerging role of MD simulations in facilitating the pharmaceutical formulation development of drugs and candidate drugs. Specifically, we look at how MD can be used in studying the crystalline and amorphous solids, the stability of amorphous drug or drug-polymer formulations, and drug solubility. Moreover, since nanoparticle drug formulations are of great interest in the field of drug delivery research, different applications of nano-particle simulations are also briefly summarized using multiple recent studies as examples. In the future, the role of MD simulations in facilitating the drug development process is likely to grow substantially with the increasing computer power and advancements in the development of force fields and enhanced MD methodologies.

Sarco(endo)plasmic reticulum Ca 2؉ ATPase (SERCA) Ca 2؉ transporters pump cytosolic Ca 2؉ into the endoplasmic reticulum, maintaining a Ca 2؉ gradient that controls vital cell functions ranging from proliferation to death. To meet the physiological demand of the cell, SERCA activity is regulated by adjusting the affinity for Ca 2؉ ions. Of all SERCA isoforms, the housekeeping SERCA2b isoform displays the highest Ca 2؉ affinity because of a unique C-terminal extension (2b-tail). Here, an extensive structure-function analysis of SERCA2b mutants and SERCA1a2b chimera revealed how the 2b-tail controls Ca 2؉ affinity. Its transmembrane (TM) segment (TM11) and luminal extension functionally cooperate and interact with TM7/TM10 and luminal loops of SERCA2b, respectively. This stabilizes the Ca 2؉ -bound E1 conformation and alters Ca 2؉ -transport kinetics, which provides the rationale for the higher apparent Ca 2؉ affinity. Based on our NMR structure of TM11 and guided by mutagenesis results, a structural model was developed for SERCA2b that supports the proposed 2b-tail mechanism and is reminiscent of the interaction between the ␣-and ␤-subunits of Na ؉ ,K ؉ -ATPase. The 2b-tail interaction site may represent a novel target to increase the Ca 2؉ affinity of malfunctioning SERCA2a in the failing heart to improve contractility.endoplasmic reticulum ͉ Ca 2ϩ -ATPase ͉ ion transporter ͉ phospholamban ͉ P-type ATPase C alcium ions in the endoplasmic reticulum (ER) control cellular growth, proliferation, differentiation, and death and are maintained at high concentrations by the ubiquitous ER Ca 2ϩ pump sarco(endo)plasmic reticulum Ca 2ϩ ATPase 2b (SERCA2b) (1). SERCAs cycle between an E1 conformation, with high-affinity Ca 2ϩ -binding sites facing the cytoplasm, and E2 with low-affinity Ca 2ϩ -binding sites facing the lumen of the ER (2, 3). Several 3D crystal structures of SERCA1a, the related fast-twitch skeletal-muscle isoform, provided detailed insights into the mechanism of Ca 2ϩ transport. Conformational changes in the cytosolic domain of the pump are driven by ATP hydrolysis and control the opening and closing of the Ca 2ϩ gates in the transmembrane (TM) domain. The TM region contains 10 TM helices comprising residues that reversibly coordinate Ca 2ϩ for transport (4-7) (reviewed in ref. 3).Unfortunately, much less is known about the structure and mechanism of the ubiquitous SERCA2 isoform (Ϸ84% sequence identity with SERCA1a). Alternative splicing of the SERCA2 messenger yields two variants: SERCA2a, which populates the sarcoplasmic reticulum (SR) of the heart, smooth, and slow-twitch skeletal muscle; and the housekeeping variant SERCA2b, which is present in the ER of all cell types (Fig. S1a) (8). SERCA2b differs from the muscle isoforms SERCA1a or SERCA2a, displaying a 2-fold higher affinity for Ca 2ϩ and lower catalytic turnover rate. These unique functional properties are related to an extended C terminus of 49 residues (2b-tail) containing an 11th TM domain (TM11) and luminal extension (LE) (Fig. S1b) (9-12), b...